Abstract
Bioinformatics plays an important role in natural sciences. One of its branches – Computer-Aided Drug Design (CADD) – gives practical insights for designing and discovering of novel – better and safer – drugs. The CADD encompasses many different techniques like docking, virtual screening and quantitative structure-activity relationships (QSAR). The latter deals with building equations relating drug activities and their structures represented by variables called molecular descriptors. An important and promising type of such descriptors are Sinister-Rectus Chirality Measures (SRCM). However, the only so far available software for \(^{SR}CM\) calculation is very slow, and this impedes wider application of \(^{SR}CM\) by QSAR community. Therefore, an attempt to develop a novel algorithm for calculation of \(^{SR}CM\) (using Genetic Algorithm) and to implement it in an efficient and modern computer program was made. The result of these efforts is Chirmes. Performed tests have shown that Chirmes gives correct results of \(^{SR}CM\) calculations and performs way faster than the so far available software does. The paper describes first chemical and computational background behind the tackled problem. Then details of the implementation are presented, along with the test results and future prospects.
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Notes
- 1.
Usage of real numbers was inspired by [8].
- 2.
Period of algorithm is \(2^{19937} - 1\) which is more than enough for generating random population. Moreover, it is well known and optimized.
- 3.
Strong selective pressure make algorithm to convergence to early, from the other side, weak pressure searching less effective. It is important to find correct bias between too strong and too weak pressure [8].
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Szurmak, P., Mulawka, J. (2017). New Method of Calculating \(^{SR}CM\) Chirality Measure. In: Kryszkiewicz, M., Appice, A., Ślęzak, D., Rybinski, H., Skowron, A., Raś, Z. (eds) Foundations of Intelligent Systems. ISMIS 2017. Lecture Notes in Computer Science(), vol 10352. Springer, Cham. https://doi.org/10.1007/978-3-319-60438-1_7
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DOI: https://doi.org/10.1007/978-3-319-60438-1_7
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